Research
Banks CAS, Boanca G, Lee ZT, Florens L, Washburn MP. Proteins interacting with cloning scars: a source of false positive protein-protein interactions. Sci Rep.2015;5:8530. doi:10.1038/srep08530. Abstract
Sardiu ME, Gilmore JM, Groppe BD, Herman D, Ramisetty SR, Cai Y, Jin J, Conaway RC, Conaway JW, Florens L, Washburn MP. Conserved abundance and topological features in chromatin-remodeling protein interaction networks. EMBO Rep.2015;16:116-126. Abstract
Sardiu ME, Smith KT, Groppe BD, Gilmore JM, Saraf A, Egidy R, Peak A, Seidel CW, Florens L, Workman JL, Washburn MP. Suberoylanilide Hydroxamic Acid (SAHA)-Induced Dynamics of a Human Histone Deacetylase Protein Interaction Network. Mol Cell Proteomics.2014;13:3114-3125.
Abstract | Original Data
Banks CA, Lee ZT, Boanca G, Lakshminarasimhan M, Groppe BD, Wen Z, Hattem GL, Seidel CW, Florens L, Washburn MP. Controlling for gene expression changes in transcription factor protein networks. Mol Cell Proteomics.2014;13:1510-1522. Abstract | Original Data
Mosley AL, Hunter GO, Sardiu ME, Smolle M, Workman JL, Florens L, Washburn MP. Quantitative Proteomics Demonstrates That the RNA Polymerase II Subunits Rpb4 and Rpb7 Dissociate during Transcriptional Elongation. Mol Cell Proteomics. 2013;12:1530-1538. Abstract | Original Data
Daniels DL, Mendez J, Mosley AL, Ramisetty SR, Murphy N, Benink H, Wood KV, Urh M, Washburn MP. Examining the complexity of human RNA polymerase complexes using HaloTag technology coupled to label free quantitative proteomics. J Proteome Res.2012;11:564-575. Abstract
Zhang Y, Wen Z, Washburn MP, Florens L. Improving proteomics mass accuracy by dynamic offline lock mass. Anal Chem.2011;83:9344-9351. Abstract
Lee KK, Sardiu ME, Swanson SK, Gilmore JM, Torok M, Grant PA, Florens L, Workman JL, Washburn MP. Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes. Mol Syst Biol.2011;7:503. Abstract
Mosley AL, Sardiu ME, Pattenden SG, Workman JL, Florens L, Washburn MP. Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes. Mol Cell Proteomics.2011;10:M110 000687. Abstract
Zhang Y, Wen Z, Washburn MP, Florens L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem.2010;82:2272-2281. Abstract
Fournier ML, Paulson A, Pavelka N, Mosley AL, Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, Seidel C, Florens L, Washburn MP. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol Cell Proteomics.2010;9:271-284. Abstract
Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP. Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One.2009;4:e7310. Abstract
Mosley AL, Pattenden SG, Carey M, Venkatesh S, Gilmore JM, Florens L, Workman JL, Washburn MP. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell.2009;34:168-178. Abstract
Zhang Y, Wen Z, Washburn MP, Florens L. Effect of dynamic exclusion duration on spectral count based quantitative proteomics. Anal Chem.2009;81:6317-6326. Abstract
Sardiu ME, Florens L, Washburn MP. Evaluation of clustering algorithms for protein complex and protein interaction network assembly. J Proteome Res.2009;8:2944-2952. Abstract
Mosley AL, Florens L, Wen Z, Washburn MP. A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus. J Proteomics.2009;72:110-120. Abstract
Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics.2008; 7(4): 631-644. Abstract
Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP. Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A.2008;105:1454-1459. Abstract
Zybailov BL, Florens L, Washburn MP. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst.2007;3:354-360. Abstract
Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A.2006;103:18928-18933. Abstract
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res.2006;5:2339-2347. Abstract
Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem.2005;77:6218-6224. Abstract
Reviews
Banks CA, Kong SE, Washburn MP. Affinity purification of protein complexes for analysis by multidimensional protein identification technology. Protein Expr Purif. 2012;86:105-119. Abstract
Sardiu ME, Washburn MP. Building protein-protein interaction networks with proteomics and informatics tools. J Biol Chem.2011;286:23645-23651. Abstract
Ramisetty SR, Washburn MP. Unraveling the dynamics of protein interactions with quantitative mass spectrometry. Crit Rev Biochem Mol Biol.2011;46:216-228. Abstract
Washburn MP. Driving biochemical discovery with quantitative proteomics. Trends Biochem Sci.2011;36:170-177. Abstract
Gilmore JM, Washburn MP. Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics.2010;73:2078-2091. Abstract
Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional Separations-Based Shotgun Proteomics. Chem Rev.2007;107:3654-3686. Abstract
Collaborations
Herz HM, Morgan M, Gao X, Jackson J, Rickels R, Swanson SK, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling. Science. 2014;345:1065-1070. Abstract | Original Data
D'Angiolella V, Donato V, Forrester FM, Jeong Y-T, Kudo Y, Pellacani C, Saraf A, Florens L, Washburn MP, Pagano M. The Cyclin F-Ribonucleotide Reductase M2 axis controls genome integrity and DNA repair. Cell. 2012;149:1023-1034. Abstract | Original Data
Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CA, Kong SE, Szutorisz H, Swanson SK, Martin-Brown S, Washburn MP, Florens L, Seidel CW, Lin C, Smith ER, Shilatifard A, Conaway RC, Conaway JW. Human Mediator Subunit MED26 Functions as a Docking Site for Transcription Elongation Factors. Cell.2011;146:92-104. Abstract
Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, Florens L, Washburn MP, Skowronski J. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature.2011;474:658-661. Abstract
Suganuma T, Mushegian A, Swanson SK, Abmayr SM, Florens L, Washburn MP, Workman JL. The ATAC acetyltransferase complex coordinates MAP kinases to regulate JNK target genes. Cell.2010;142:726-736. Abstract
D'Angiolella V, Donato V, Vijayakumar S, Saraf A, Florens L, Washburn MP, Dynlacht B, Pagano M. SCF(Cyclin F) controls centrosome homeostasis and mitotic fidelity through CP110 degradation. Nature.2010;466:138-142. Abstract
Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell.2007;131:1084-1096. Abstract
Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell.2005;123:581-592. Abstract
Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates Iii JR, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science.2004;306:2084-2087. Abstract.